Phenotype SNPs from prehistoric sub-Saharan Africa

Below are derived allele counts and total numbers of reads for SNPs that have a large effect on phenotype for 15 genomes from prehistoric sub-Saharan Africa. Nonzero derived allele counts are highlighted. Note that small derived allele counts may be due to DNA damage.

ASIP, rs2424984, Veddoid brown skin

Sample Location Date D/T
I9028 South Africa 291–15 BC 0/1
I9133 South Africa 67 BC – 202 AD 0/3
I9134 South Africa 668–881 AD 0/1

ASIP, rs6058017, Veddoid brown skin

Sample Location Date D/T
I9028 South Africa 291–15 BC 4/5
I9133 South Africa 67 BC – 202 AD 0/1
I2298 Tanzania 1311–1406 AD 0/1

EDAR, rs3827760, Mongoloid teeth, hair, etc.

Sample Location Date D/T
I2966 Malawi 8050–3050 BC 0/1
I4468 Malawi 4227–3973 BC 0/1
I4426 Malawi 726–380 BC 0/7
I9133 South Africa 67 BC – 202 AD 0/2
I9134 South Africa 668–881 AD 0/1
I3726 Tanzania 1191–940 BC 0/10
I0589 Tanzania 580–647 AD 0/13
I2298 Tanzania 1311–1406 AD 0/13

IRF4, rs12203592, light hair and eyes, freckling

Sample Location Date D/T
I2966 Malawi 8050–3050 BC 0/2
I4421 Malawi 3450–2850 BC 0/1
I4426 Malawi 726–380 BC 0/2
I9028 South Africa 291–15 BC 0/1
I9133 South Africa 67 BC – 202 AD 0/1
I3726 Tanzania 1191–940 BC 0/2
I0589 Tanzania 580–647 AD 0/5
I2298 Tanzania 1311–1406 AD 0/1

KITLG, rs12821256, blond hair

Sample Location Date D/T
I9028 South Africa 291–15 BC 0/2
I9133 South Africa 67 BC – 202 AD 0/3
I0589 Tanzania 580–647 AD 0/2

KITLG, rs642742, Veddoid brown skin

Sample Location Date D/T
I9028 South Africa 291–15 BC 0/7
I9133 South Africa 67 BC – 202 AD 0/2
I9134 South Africa 668–881 AD 0/4

MC1R, rs1110400, red hair

Sample Location Date D/T
I2966 Malawi 8050–3050 BC 0/2
I4426 Malawi 726–380 BC 0/8
I9028 South Africa 291–15 BC 0/12
I9133 South Africa 67 BC – 202 AD 0/3
I9134 South Africa 668–881 AD 0/3
I3726 Tanzania 1191–940 BC 0/7
I1048 Tanzania 529–643 AD 0/1
I0589 Tanzania 580–647 AD 0/14
I2298 Tanzania 1311–1406 AD 0/11

MC1R, rs11547464, red hair

Sample Location Date D/T
I2966 Malawi 8050–3050 BC 0/1
I4421 Malawi 3450–2850 BC 0/1
I4426 Malawi 726–380 BC 1/9
I9028 South Africa 291–15 BC 1/8
I9133 South Africa 67 BC – 202 AD 0/2
I3726 Tanzania 1191–940 BC 0/7
I1048 Tanzania 529–643 AD 1/1
I0589 Tanzania 580–647 AD 0/7
I2298 Tanzania 1311–1406 AD 0/11

MC1R, rs1805005, blond hair, fair skin

Sample Location Date D/T
I2966 Malawi 8050–3050 BC 0/1
I4426 Malawi 726–380 BC 0/2
I9028 South Africa 291–15 BC 0/13
I9134 South Africa 668–881 AD 1/3
I3726 Tanzania 1191–940 BC 2/2
I0589 Tanzania 580–647 AD 0/5
I2298 Tanzania 1311–1406 AD 0/2

MC1R, rs1805006, red hair, fair skin

Sample Location Date D/T
I2967 Malawi 6223–6007 BC 0/1
I2966 Malawi 8050–3050 BC 0/5
I4426 Malawi 726–380 BC 0/5
I9028 South Africa 291–15 BC 0/7
I9133 South Africa 67 BC – 202 AD 0/2
I9134 South Africa 668–881 AD 0/2
I3726 Tanzania 1191–940 BC 0/3
I0589 Tanzania 580–647 AD 0/8
I2298 Tanzania 1311–1406 AD 0/12
I0595 Kenya 1454–1628 AD 0/2

MC1R, rs1805007, red hair, fair skin

Sample Location Date D/T
I2966 Malawi 8050–3050 BC 0/2
I4421 Malawi 3450–2850 BC 0/1
I4426 Malawi 726–380 BC 1/9
I9028 South Africa 291–15 BC 0/2
I9133 South Africa 67 BC – 202 AD 0/2
I9134 South Africa 668–881 AD 0/2
I3726 Tanzania 1191–940 BC 0/9
I1048 Tanzania 529–643 AD 0/2
I0589 Tanzania 580–647 AD 0/11
I2298 Tanzania 1311–1406 AD 0/13

MC1R, rs1805008, red hair, fair skin

Sample Location Date D/T
I2966 Malawi 8050–3050 BC 0/1
I4426 Malawi 726–380 BC 0/7
I9028 South Africa 291–15 BC 1/37
I9133 South Africa 67 BC – 202 AD 0/4
I9134 South Africa 668–881 AD 0/4
I3726 Tanzania 1191–940 BC 0/5
I1048 Tanzania 529–643 AD 0/1
I0589 Tanzania 580–647 AD 0/9
I2298 Tanzania 1311–1406 AD 0/8

MC1R, rs1805009, red hair, fair skin

Sample Location Date D/T
I2966 Malawi 8050–3050 BC 0/2
I4426 Malawi 726–380 BC 0/6
I9028 South Africa 291–15 BC 0/3
I9133 South Africa 67 BC – 202 AD 0/4
I3726 Tanzania 1191–940 BC 0/8
I1048 Tanzania 529–643 AD 0/2
I0589 Tanzania 580–647 AD 0/11
I2298 Tanzania 1311–1406 AD 0/14
I0595 Kenya 1454–1628 AD 0/1

MCM6, rs182549, ability to digest milk

Sample Location Date D/T
I2966 Malawi 8050–3050 BC 0/3
I9028 South Africa 291–15 BC 0/2
I9133 South Africa 67 BC – 202 AD 0/6
I9134 South Africa 668–881 AD 0/1
I3726 Tanzania 1191–940 BC 0/2

MCM6, rs4988235, ability to digest milk

Sample Location Date D/T
I2966 Malawi 8050–3050 BC 0/2
I4421 Malawi 3450–2850 BC 0/2
I4426 Malawi 726–380 BC 0/3
I9133 South Africa 67 BC – 202 AD 0/1
I9134 South Africa 668–881 AD 0/1
I3726 Tanzania 1191–940 BC 0/8
I0589 Tanzania 580–647 AD 0/5
I2298 Tanzania 1311–1406 AD 0/6

OCA2, rs1800407, green or hazel eyes

Sample Location Date D/T
I2966 Malawi 8050–3050 BC 0/1
I4426 Malawi 726–380 BC 0/3
I9028 South Africa 291–15 BC 0/1
I9133 South Africa 67 BC – 202 AD 0/2
I3726 Tanzania 1191–940 BC 1/1
I1048 Tanzania 529–643 AD 0/3
I0589 Tanzania 580–647 AD 0/5
I2298 Tanzania 1311–1406 AD 0/2
I0595 Kenya 1454–1628 AD 0/1

OCA2, rs1800414, Mongoloid light skin

Sample Location Date D/T
I2966 Malawi 8050–3050 BC 0/1
I4468 Malawi 4227–3973 BC 0/1
I4426 Malawi 726–380 BC 0/1
I9133 South Africa 67 BC – 202 AD 0/2
I3726 Tanzania 1191–940 BC 0/3
I0589 Tanzania 580–647 AD 0/4
I2298 Tanzania 1311–1406 AD 0/2

OCA2/HERC2, rs12913832, blue eyes

Sample Location Date D/T
I2966 Malawi 8050–3050 BC 0/4
I4421 Malawi 3450–2850 BC 0/1
I4426 Malawi 726–380 BC 0/3
I9028 South Africa 291–15 BC 0/2
I9133 South Africa 67 BC – 202 AD 0/6
I3726 Tanzania 1191–940 BC 0/7
I0589 Tanzania 580–647 AD 0/6
I2298 Tanzania 1311–1406 AD 0/3

SLC24A5, rs1426654, Caucasoid light skin

Sample Location Date D/T
I2966 Malawi 8050–3050 BC 0/2
I9028 South Africa 291–15 BC 0/2
I9133 South Africa 67 BC – 202 AD 0/4
I3726 Tanzania 1191–940 BC 0/2

SLC45A2, rs16891982, Caucasoid light skin

Sample Location Date D/T
I2966 Malawi 8050–3050 BC 0/2
I4426 Malawi 726–380 BC 0/10
I9028 South Africa 291–15 BC 0/1
I9133 South Africa 67 BC – 202 AD 0/3
I3726 Tanzania 1191–940 BC 0/11
I0589 Tanzania 580–647 AD 0/7
I2298 Tanzania 1311–1406 AD 3/8
I0595 Kenya 1454–1628 AD 0/2

TYR, rs1042602, light skin, absence of freckles

Sample Location Date D/T
I2966 Malawi 8050–3050 BC 0/3
I4426 Malawi 726–380 BC 0/1
I9133 South Africa 67 BC – 202 AD 0/3
I9134 South Africa 668–881 AD 0/1
I3726 Tanzania 1191–940 BC 0/5
I0589 Tanzania 580–647 AD 0/6
I2298 Tanzania 1311–1406 AD 0/4

TYR, rs1393350, blond hair, blue eyes

Sample Location Date D/T
I2966 Malawi 8050–3050 BC 0/1
I4426 Malawi 726–380 BC 0/2
I9028 South Africa 291–15 BC 0/1
I9133 South Africa 67 BC – 202 AD 0/5
I9134 South Africa 668–881 AD 0/3
I3726 Tanzania 1191–940 BC 0/8
I0589 Tanzania 580–647 AD 0/4
I2298 Tanzania 1311–1406 AD 0/1

TYRP1, rs2733831, light hair and eyes

Sample Location Date D/T
I9028 South Africa 291–15 BC 0/1
I9133 South Africa 67 BC – 202 AD 0/4
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4 comments on “Phenotype SNPs from prehistoric sub-Saharan Africa
  1. capra internetensis says:

    The Tanzanian pastoralist was homozygous for the derived allele in SLC45A2 but ancestral for the SLC24A5 allele? Wouldn’t have expected that.

    Do you plan on checking for Sub-Saharan lactase persistence alleles, or would it be too much bother? rs145946881 aka C-14010 seems most likely.

    • Genetiker says:

      The Tanzanian pastoralist was homozygous for the derived allele in SLC45A2 but ancestral for the SLC24A5 allele? Wouldn’t have expected that.

      I haven’t been able to download the sequence data, so I can’t investigate how likely the derived alleles are to be genuine as opposed to the result of DNA damage. I only have the pseudo-haploid genotype data, so all the genotypes appear to be homozygous when they may not be in reality. However, rs16891982 is a transversion SNP, making it very unlikely to be affected by DNA damage.

      Do you plan on checking for Sub-Saharan lactase persistence alleles, or would it be too much bother? rs145946881 aka C-14010 seems most likely.

      The available genotype data for rs145946881:

      I2966, Malawi 5600 BC: CC
      I4468, Malawi 4100 BC: CC
      Mota, Ethiopia 2500 BC: CC
      I9133, South Africa 100 AD: CC

      None of them have the derived G allele.

  2. capra internetensis says:

    Thanks! Very interesting.

  3. Genetiker says:

    I’ve updated this post to give derived allele counts instead of genotypes.

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